Goal: Do an MDS plot using Irene’s SNPs to look for relatedness among plants

Snp calling with freebayes

First, need to call SNPs using all BAM files at once:

working in directory 2019/IreneSnps on whitney

first, sort bams

for f in SNPanalysis/*LT*rmdup.bam
    do 
       newname=`basename $f .bam`_sort.bam
       samtools sort -o $newname --reference SNPanalysis/Pinsaporeference1 $f 
    done

next, assign read groups to bams

input=""

for f in `ls *sort.bam`
   do
      rg=`basename $f _rmdup_sort.bam`
      input="$input -b $f -r $rg -s $rg"
  done

echo $input

bamaddrg $input > LT_rmdup_sort_combined.bam

samtools index LT_rmdup_sort_combined.bam
freebayes -f SNPanalysis/Pinsaporeference1 --no-indels --no-mnps --no-complex LT_rmdup_sort_combined.bam > LT.vcf &

try parallel

ulimit -n 4000
/usr/local/stow/freebayes/scripts/fasta_generate_regions.py Pinsaporeference1.fai 100000 > regions
./freebayes-parallel regions 8 -f Pinsaporeference1 --no-indels --no-mnps --no-complex LT_rmdup_sort_combined.bam > LT.vcf 

(note: I edited the freebayes-parallel script so that it would work…)

Freeybayes parallel takes about 12 hours

try parallel, keep snps

ulimit -n 4000
/usr/local/stow/freebayes/scripts/fasta_generate_regions.py Pinsaporeference1.fai 100000 > regions
./freebayes-parallel regions 8 -f Pinsaporeference1 --no-mnps --no-complex LT_rmdup_sort_combined.bam > LT_w_indel.vcf 
scp whitney.plb.ucdavis.edu:2019/IreneSnps/LT.vcf.gz ../input/

now analyze vcf in R

library(tidyverse)
── Attaching packages ───────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.0.0     ✔ purrr   0.2.5
✔ tibble  1.4.2     ✔ dplyr   0.7.6
✔ tidyr   0.8.1     ✔ stringr 1.3.1
✔ readr   1.1.1     ✔ forcats 0.3.0
── Conflicts ──────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
library(ggrepel)

get the vcf header

vcf.header <- system("zgrep '#C' ../input/LT.vcf.gz",intern = TRUE) 
vcf.header
[1] "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t38LTR\t42LTR\t42LTRR\t43LTR\t43LTRR\t49LTWR\t49LTWRR\t95LTWR\t95LTWRR\t99LTWR"
vcf.header <- vcf.header %>% 
  str_replace("#","") %>% #get rid of the pound sign
  str_split(pattern = "\t") %>% #split on the tabs
  magrittr::extract2(1)
vcf.header
 [1] "CHROM"   "POS"     "ID"      "REF"     "ALT"     "QUAL"    "FILTER"  "INFO"   
 [9] "FORMAT"  "38LTR"   "42LTR"   "42LTRR"  "43LTR"   "43LTRR"  "49LTWR"  "49LTWRR"
[17] "95LTWR"  "95LTWRR" "99LTWR" 

get the data

snps <- read_tsv("../input/LT.vcf.gz", na = c("","NA","."),comment="#",col_names = vcf.header) %>%
  select(-ID, -FILTER) # these are empty columns
Parsed with column specification:
cols(
  CHROM = col_character(),
  POS = col_integer(),
  ID = col_character(),
  REF = col_character(),
  ALT = col_character(),
  QUAL = col_double(),
  FILTER = col_character(),
  INFO = col_character(),
  FORMAT = col_character(),
  `38LTR` = col_character(),
  `42LTR` = col_character(),
  `42LTRR` = col_character(),
  `43LTR` = col_character(),
  `43LTRR` = col_character(),
  `49LTWR` = col_character(),
  `49LTWRR` = col_character(),
  `95LTWR` = col_character(),
  `95LTWRR` = col_character(),
  `99LTWR` = col_character()
)

|==                                                                        |   3%   13 MB
|==                                                                        |   3%   13 MB
|==                                                                        |   3%   13 MB
|==                                                                        |   3%   14 MB
|==                                                                        |   3%   14 MB
|==                                                                        |   3%   15 MB
|==                                                                        |   3%   15 MB
|==                                                                        |   3%   15 MB
|===                                                                       |   4%   16 MB
|===                                                                       |   4%   16 MB
|===                                                                       |   4%   16 MB
|===                                                                       |   4%   17 MB
|===                                                                       |   4%   17 MB
|===                                                                       |   4%   18 MB
|===                                                                       |   4%   18 MB
|===                                                                       |   4%   18 MB
|===                                                                       |   4%   19 MB
|===                                                                       |   4%   19 MB
|===                                                                       |   5%   20 MB
|===                                                                       |   5%   20 MB
|===                                                                       |   5%   20 MB
|===                                                                       |   5%   21 MB
|====                                                                      |   5%   21 MB
|====                                                                      |   5%   21 MB
|====                                                                      |   5%   22 MB
|====                                                                      |   5%   22 MB
|====                                                                      |   5%   23 MB
|====                                                                      |   5%   23 MB
|====                                                                      |   6%   24 MB
|====                                                                      |   6%   24 MB
|====                                                                      |   6%   24 MB
|====                                                                      |   6%   25 MB
|====                                                                      |   6%   25 MB
|====                                                                      |   6%   25 MB
|====                                                                      |   6%   26 MB
|=====                                                                     |   6%   26 MB
|=====                                                                     |   6%   27 MB
|=====                                                                     |   6%   27 MB
|=====                                                                     |   6%   27 MB
|=====                                                                     |   7%   28 MB
|=====                                                                     |   7%   28 MB
|=====                                                                     |   7%   29 MB
|=====                                                                     |   7%   29 MB
|=====                                                                     |   7%   29 MB
|=====                                                                     |   7%   30 MB
|=====                                                                     |   7%   30 MB
|=====                                                                     |   7%   30 MB
|=====                                                                     |   7%   31 MB
|=====                                                                     |   7%   31 MB
|======                                                                    |   8%   32 MB
|======                                                                    |   8%   32 MB
|======                                                                    |   8%   32 MB
|======                                                                    |   8%   33 MB
|======                                                                    |   8%   33 MB
|======                                                                    |   8%   34 MB
|======                                                                    |   8%   34 MB
|======                                                                    |   8%   34 MB
|======                                                                    |   8%   35 MB
|======                                                                    |   8%   35 MB
|======                                                                    |   9%   36 MB
|======                                                                    |   9%   36 MB
|======                                                                    |   9%   36 MB
|======                                                                    |   9%   37 MB
|=======                                                                   |   9%   37 MB
|=======                                                                   |   9%   37 MB
|=======                                                                   |   9%   38 MB
|=======                                                                   |   9%   38 MB
|=======                                                                   |   9%   39 MB
|=======                                                                   |   9%   39 MB
|=======                                                                   |   9%   39 MB
|=======                                                                   |  10%   40 MB
|=======                                                                   |  10%   40 MB
|=======                                                                   |  10%   40 MB
|=======                                                                   |  10%   41 MB
|=======                                                                   |  10%   41 MB
|=======                                                                   |  10%   42 MB
|=======                                                                   |  10%   42 MB
|========                                                                  |  10%   42 MB
|========                                                                  |  10%   43 MB
|========                                                                  |  10%   43 MB
|========                                                                  |  11%   44 MB
|========                                                                  |  11%   44 MB
|========                                                                  |  11%   44 MB
|========                                                                  |  11%   45 MB
|========                                                                  |  11%   45 MB
|========                                                                  |  11%   46 MB
|========                                                                  |  11%   46 MB
|========                                                                  |  11%   46 MB
|========                                                                  |  11%   47 MB
|========                                                                  |  11%   47 MB
|=========                                                                 |  12%   47 MB
|=========                                                                 |  12%   48 MB
|=========                                                                 |  12%   48 MB
|=========                                                                 |  12%   49 MB
|=========                                                                 |  12%   49 MB
|=========                                                                 |  12%   49 MB
|=========                                                                 |  12%   50 MB
|=========                                                                 |  12%   50 MB
|=========                                                                 |  12%   51 MB
|=========                                                                 |  12%   51 MB
|=========                                                                 |  12%   51 MB
|=========                                                                 |  13%   52 MB
|=========                                                                 |  13%   52 MB
|=========                                                                 |  13%   53 MB
|==========                                                                |  13%   53 MB
|==========                                                                |  13%   53 MB
|==========                                                                |  13%   54 MB
|==========                                                                |  13%   54 MB
|==========                                                                |  13%   54 MB
|==========                                                                |  13%   55 MB
|==========                                                                |  13%   55 MB
|==========                                                                |  14%   56 MB
|==========                                                                |  14%   56 MB
|==========                                                                |  14%   56 MB
|==========                                                                |  14%   57 MB
|==========                                                                |  14%   57 MB
|==========                                                                |  14%   57 MB
|==========                                                                |  14%   58 MB
|===========                                                               |  14%   58 MB
|===========                                                               |  14%   59 MB
|===========                                                               |  14%   59 MB
|===========                                                               |  15%   59 MB
|===========                                                               |  15%   60 MB
|===========                                                               |  15%   60 MB
|===========                                                               |  15%   61 MB
|===========                                                               |  15%   61 MB
|===========                                                               |  15%   61 MB
|===========                                                               |  15%   62 MB
|===========                                                               |  15%   62 MB
|===========                                                               |  15%   63 MB
|===========                                                               |  15%   63 MB
|===========                                                               |  15%   63 MB
|============                                                              |  16%   64 MB
|============                                                              |  16%   64 MB
|============                                                              |  16%   64 MB
|============                                                              |  16%   65 MB
|============                                                              |  16%   65 MB
|============                                                              |  16%   66 MB
|============                                                              |  16%   66 MB
|============                                                              |  16%   66 MB
|============                                                              |  16%   67 MB
|============                                                              |  16%   67 MB
|============                                                              |  17%   68 MB
|============                                                              |  17%   68 MB
|============                                                              |  17%   68 MB
|=============                                                             |  17%   69 MB
|=============                                                             |  17%   69 MB
|=============                                                             |  17%   69 MB
|=============                                                             |  17%   70 MB
|=============                                                             |  17%   70 MB
|=============                                                             |  17%   71 MB
|=============                                                             |  17%   71 MB
|=============                                                             |  18%   71 MB
|=============                                                             |  18%   72 MB
|=============                                                             |  18%   72 MB
|=============                                                             |  18%   73 MB
|=============                                                             |  18%   73 MB
|=============                                                             |  18%   73 MB
|=============                                                             |  18%   74 MB
|==============                                                            |  18%   74 MB
|==============                                                            |  18%   74 MB
|==============                                                            |  18%   75 MB
|==============                                                            |  18%   75 MB
|==============                                                            |  19%   76 MB
|==============                                                            |  19%   76 MB
|==============                                                            |  19%   76 MB
|==============                                                            |  19%   77 MB
|==============                                                            |  19%   77 MB
|==============                                                            |  19%   78 MB
|==============                                                            |  19%   78 MB
|==============                                                            |  19%   78 MB
|==============                                                            |  19%   79 MB
|==============                                                            |  19%   79 MB
|===============                                                           |  20%   79 MB
|===============                                                           |  20%   80 MB
|===============                                                           |  20%   80 MB
|===============                                                           |  20%   81 MB
|===============                                                           |  20%   81 MB
|===============                                                           |  20%   81 MB
|===============                                                           |  20%   82 MB
|===============                                                           |  20%   82 MB
|===============                                                           |  20%   83 MB
|===============                                                           |  20%   83 MB
|===============                                                           |  21%   83 MB
|===============                                                           |  21%   84 MB
|===============                                                           |  21%   84 MB
|===============                                                           |  21%   84 MB
|================                                                          |  21%   85 MB
|================                                                          |  21%   85 MB
|================                                                          |  21%   86 MB
|================                                                          |  21%   86 MB
|================                                                          |  21%   86 MB
|================                                                          |  21%   87 MB
|================                                                          |  21%   87 MB
|================                                                          |  22%   87 MB
|================                                                          |  22%   88 MB
|================                                                          |  22%   88 MB
|================                                                          |  22%   89 MB
|================                                                          |  22%   89 MB
|================                                                          |  22%   89 MB
|================                                                          |  22%   90 MB
|=================                                                         |  22%   90 MB
|=================                                                         |  22%   91 MB
|=================                                                         |  22%   91 MB
|=================                                                         |  23%   91 MB
|=================                                                         |  23%   92 MB
|=================                                                         |  23%   92 MB
|=================                                                         |  23%   92 MB
|=================                                                         |  23%   93 MB
|=================                                                         |  23%   93 MB
|=================                                                         |  23%   94 MB
|=================                                                         |  23%   94 MB
|=================                                                         |  23%   94 MB
|=================                                                         |  23%   95 MB
|=================                                                         |  23%   95 MB
|==================                                                        |  24%   95 MB
|==================                                                        |  24%   96 MB
|==================                                                        |  24%   96 MB
|==================                                                        |  24%   97 MB
|==================                                                        |  24%   97 MB
|==================                                                        |  24%   97 MB
|==================                                                        |  24%   98 MB
|==================                                                        |  24%   98 MB
|==================                                                        |  24%   99 MB
|==================                                                        |  24%   99 MB
|==================                                                        |  25%   99 MB
|==================                                                        |  25%  100 MB
|==================                                                        |  25%  100 MB
|==================                                                        |  25%  100 MB
|===================                                                       |  25%  101 MB
|===================                                                       |  25%  101 MB
|===================                                                       |  25%  102 MB
|===================                                                       |  25%  102 MB
|===================                                                       |  25%  102 MB
|===================                                                       |  25%  103 MB
|===================                                                       |  25%  103 MB
|===================                                                       |  26%  104 MB
|===================                                                       |  26%  104 MB
|===================                                                       |  26%  104 MB
|===================                                                       |  26%  105 MB
|===================                                                       |  26%  105 MB
|===================                                                       |  26%  105 MB
|===================                                                       |  26%  106 MB
|====================                                                      |  26%  106 MB
|====================                                                      |  26%  107 MB
|====================                                                      |  26%  107 MB
|====================                                                      |  27%  107 MB
|====================                                                      |  27%  108 MB
|====================                                                      |  27%  108 MB
|====================                                                      |  27%  109 MB
|====================                                                      |  27%  109 MB
|====================                                                      |  27%  109 MB
|====================                                                      |  27%  110 MB
|====================                                                      |  27%  110 MB
|====================                                                      |  27%  110 MB
|====================                                                      |  27%  111 MB
|====================                                                      |  27%  111 MB
|=====================                                                     |  28%  112 MB
|=====================                                                     |  28%  112 MB
|=====================                                                     |  28%  112 MB
|=====================                                                     |  28%  113 MB
|=====================                                                     |  28%  113 MB
|=====================                                                     |  28%  114 MB
|=====================                                                     |  28%  114 MB
|=====================                                                     |  28%  114 MB
|=====================                                                     |  28%  115 MB
|=====================                                                     |  28%  115 MB
|=====================                                                     |  29%  116 MB
|=====================                                                     |  29%  116 MB
|=====================                                                     |  29%  116 MB
|======================                                                    |  29%  117 MB
|======================                                                    |  29%  117 MB
|======================                                                    |  29%  117 MB
|======================                                                    |  29%  118 MB
|======================                                                    |  29%  118 MB
|======================                                                    |  29%  119 MB
|======================                                                    |  29%  119 MB
|======================                                                    |  30%  119 MB
|======================                                                    |  30%  120 MB
|======================                                                    |  30%  120 MB
|======================                                                    |  30%  121 MB
|======================                                                    |  30%  121 MB
|======================                                                    |  30%  121 MB
|======================                                                    |  30%  122 MB
|=======================                                                   |  30%  122 MB
|=======================                                                   |  30%  122 MB
|=======================                                                   |  30%  123 MB
|=======================                                                   |  31%  123 MB
|=======================                                                   |  31%  124 MB
|=======================                                                   |  31%  124 MB
|=======================                                                   |  31%  124 MB
|=======================                                                   |  31%  125 MB
|=======================                                                   |  31%  125 MB
|=======================                                                   |  31%  126 MB
|=======================                                                   |  31%  126 MB
|=======================                                                   |  31%  126 MB
|=======================                                                   |  31%  127 MB
|=======================                                                   |  31%  127 MB
|========================                                                  |  32%  128 MB
|========================                                                  |  32%  128 MB
|========================                                                  |  32%  128 MB
|========================                                                  |  32%  129 MB
|========================                                                  |  32%  129 MB
|========================                                                  |  32%  129 MB
|========================                                                  |  32%  130 MB
|========================                                                  |  32%  130 MB
|========================                                                  |  32%  131 MB
|========================                                                  |  32%  131 MB
|========================                                                  |  33%  131 MB
|========================                                                  |  33%  132 MB
|========================                                                  |  33%  132 MB
|=========================                                                 |  33%  133 MB
|=========================                                                 |  33%  133 MB
|=========================                                                 |  33%  133 MB
|=========================                                                 |  33%  134 MB
|=========================                                                 |  33%  134 MB
|=========================                                                 |  33%  135 MB
|=========================                                                 |  33%  135 MB
|=========================                                                 |  34%  135 MB
|=========================                                                 |  34%  136 MB
|=========================                                                 |  34%  136 MB
|=========================                                                 |  34%  137 MB
|=========================                                                 |  34%  137 MB
|=========================                                                 |  34%  137 MB
|=========================                                                 |  34%  138 MB
|==========================                                                |  34%  138 MB
|==========================                                                |  34%  139 MB
|==========================                                                |  34%  139 MB
|==========================                                                |  35%  139 MB
|==========================                                                |  35%  140 MB
|==========================                                                |  35%  140 MB
|==========================                                                |  35%  141 MB
|==========================                                                |  35%  141 MB
|==========================                                                |  35%  141 MB
|==========================                                                |  35%  142 MB
|==========================                                                |  35%  142 MB
|==========================                                                |  35%  142 MB
|==========================                                                |  35%  143 MB
|===========================                                               |  36%  143 MB
|===========================                                               |  36%  144 MB
|===========================                                               |  36%  144 MB
|===========================                                               |  36%  144 MB
|===========================                                               |  36%  145 MB
|===========================                                               |  36%  145 MB
|===========================                                               |  36%  146 MB
|===========================                                               |  36%  146 MB
|===========================                                               |  36%  146 MB
|===========================                                               |  36%  147 MB
|===========================                                               |  37%  147 MB
|===========================                                               |  37%  148 MB
|===========================                                               |  37%  148 MB
|===========================                                               |  37%  148 MB
|============================                                              |  37%  149 MB
|============================                                              |  37%  149 MB
|============================                                              |  37%  150 MB
|============================                                              |  37%  150 MB
|============================                                              |  37%  150 MB
|============================                                              |  37%  151 MB
|============================                                              |  37%  151 MB
|============================                                              |  38%  151 MB
|============================                                              |  38%  152 MB
|============================                                              |  38%  152 MB
|============================                                              |  38%  153 MB
|============================                                              |  38%  153 MB
|============================                                              |  38%  153 MB
|=============================                                             |  38%  154 MB
|=============================                                             |  38%  154 MB
|=============================                                             |  38%  155 MB
|=============================                                             |  38%  155 MB
|=============================                                             |  39%  155 MB
|=============================                                             |  39%  156 MB
|=============================                                             |  39%  156 MB
|=============================                                             |  39%  157 MB
|=============================                                             |  39%  157 MB
|=============================                                             |  39%  157 MB
|=============================                                             |  39%  158 MB
|=============================                                             |  39%  158 MB
|=============================                                             |  39%  159 MB
|=============================                                             |  39%  159 MB
|==============================                                            |  40%  159 MB
|==============================                                            |  40%  160 MB
|==============================                                            |  40%  160 MB
|==============================                                            |  40%  160 MB
|==============================                                            |  40%  161 MB
|==============================                                            |  40%  161 MB
|==============================                                            |  40%  162 MB
|==============================                                            |  40%  162 MB
|==============================                                            |  40%  162 MB
|==============================                                            |  40%  163 MB
|==============================                                            |  41%  163 MB
|==============================                                            |  41%  164 MB
|==============================                                            |  41%  164 MB
|===============================                                           |  41%  164 MB
|===============================                                           |  41%  165 MB
|===============================                                           |  41%  165 MB
|===============================                                           |  41%  166 MB
|===============================                                           |  41%  166 MB
|===============================                                           |  41%  166 MB
|===============================                                           |  41%  167 MB
|===============================                                           |  42%  167 MB
|===============================                                           |  42%  168 MB
|===============================                                           |  42%  168 MB
|===============================                                           |  42%  168 MB
|===============================                                           |  42%  169 MB
|===============================                                           |  42%  169 MB
|================================                                          |  42%  170 MB
|================================                                          |  42%  170 MB
|================================                                          |  42%  171 MB
|================================                                          |  42%  171 MB
|================================                                          |  43%  171 MB
|================================                                          |  43%  172 MB
|================================                                          |  43%  172 MB
|================================                                          |  43%  173 MB
|================================                                          |  43%  173 MB
|================================                                          |  43%  173 MB
|================================                                          |  43%  174 MB
|================================                                          |  43%  174 MB
|================================                                          |  43%  175 MB
|=================================                                         |  44%  175 MB
|=================================                                         |  44%  175 MB
|=================================                                         |  44%  176 MB
|=================================                                         |  44%  176 MB
|=================================                                         |  44%  177 MB
|=================================                                         |  44%  177 MB
|=================================                                         |  44%  177 MB
|=================================                                         |  44%  178 MB
|=================================                                         |  44%  178 MB
|=================================                                         |  44%  179 MB
|=================================                                         |  44%  179 MB
|=================================                                         |  45%  179 MB
|=================================                                         |  45%  180 MB
|=================================                                         |  45%  180 MB
|==================================                                        |  45%  181 MB
|==================================                                        |  45%  181 MB
|==================================                                        |  45%  181 MB
|==================================                                        |  45%  182 MB
|==================================                                        |  45%  182 MB
|==================================                                        |  45%  183 MB
|==================================                                        |  46%  183 MB
|==================================                                        |  46%  183 MB
|==================================                                        |  46%  184 MB
|==================================                                        |  46%  184 MB
|==================================                                        |  46%  185 MB
|==================================                                        |  46%  185 MB
|==================================                                        |  46%  185 MB
|===================================                                       |  46%  186 MB
|===================================                                       |  46%  186 MB
|===================================                                       |  46%  187 MB
|===================================                                       |  46%  187 MB
|===================================                                       |  47%  187 MB
|===================================                                       |  47%  188 MB
|===================================                                       |  47%  188 MB
|===================================                                       |  47%  188 MB
|===================================                                       |  47%  189 MB
|===================================                                       |  47%  189 MB
|===================================                                       |  47%  190 MB
|===================================                                       |  47%  190 MB
|===================================                                       |  47%  190 MB
|===================================                                       |  47%  191 MB
|====================================                                      |  48%  191 MB
|====================================                                      |  48%  192 MB
|====================================                                      |  48%  192 MB
|====================================                                      |  48%  193 MB
|====================================                                      |  48%  193 MB
|====================================                                      |  48%  193 MB
|====================================                                      |  48%  194 MB
|====================================                                      |  48%  194 MB
|====================================                                      |  48%  194 MB
|====================================                                      |  48%  195 MB
|====================================                                      |  49%  195 MB
|====================================                                      |  49%  196 MB
|====================================                                      |  49%  196 MB
|=====================================                                     |  49%  196 MB
|=====================================                                     |  49%  197 MB
|=====================================                                     |  49%  197 MB
|=====================================                                     |  49%  198 MB
|=====================================                                     |  49%  198 MB
|=====================================                                     |  49%  199 MB
|=====================================                                     |  49%  199 MB
|=====================================                                     |  50%  199 MB
|=====================================                                     |  50%  200 MB
|=====================================                                     |  50%  200 MB
|=====================================                                     |  50%  201 MB
|=====================================                                     |  50%  201 MB
|=====================================                                     |  50%  201 MB
|======================================                                    |  50%  202 MB
|======================================                                    |  50%  202 MB
|======================================                                    |  50%  203 MB
|======================================                                    |  50%  203 MB
|======================================                                    |  51%  203 MB
|======================================                                    |  51%  204 MB
|======================================                                    |  51%  204 MB
|======================================                                    |  51%  204 MB
|======================================                                    |  51%  205 MB
|======================================                                    |  51%  205 MB
|======================================                                    |  51%  206 MB
|======================================                                    |  51%  206 MB
|======================================                                    |  51%  206 MB
|======================================                                    |  51%  207 MB
|=======================================                                   |  52%  207 MB
|=======================================                                   |  52%  208 MB
|=======================================                                   |  52%  208 MB
|=======================================                                   |  52%  208 MB
|=======================================                                   |  52%  209 MB
|=======================================                                   |  52%  209 MB
|=======================================                                   |  52%  210 MB
|=======================================                                   |  52%  210 MB
|=======================================                                   |  52%  210 MB
|=======================================                                   |  52%  211 MB
|=======================================                                   |  53%  211 MB
|=======================================                                   |  53%  212 MB
|=======================================                                   |  53%  212 MB
|========================================                                  |  53%  212 MB
|========================================                                  |  53%  213 MB
|========================================                                  |  53%  213 MB
|========================================                                  |  53%  213 MB
|========================================                                  |  53%  214 MB
|========================================                                  |  53%  214 MB
|========================================                                  |  53%  215 MB
|========================================                                  |  54%  215 MB
|========================================                                  |  54%  216 MB
|========================================                                  |  54%  216 MB
|========================================                                  |  54%  216 MB
|========================================                                  |  54%  217 MB
|========================================                                  |  54%  217 MB
|========================================                                  |  54%  217 MB
|=========================================                                 |  54%  218 MB
|=========================================                                 |  54%  218 MB
|=========================================                                 |  54%  219 MB
|=========================================                                 |  55%  219 MB
|=========================================                                 |  55%  219 MB
|=========================================                                 |  55%  220 MB
|=========================================                                 |  55%  220 MB
|=========================================                                 |  55%  221 MB
|=========================================                                 |  55%  221 MB
|=========================================                                 |  55%  221 MB
|=========================================                                 |  55%  222 MB
|=========================================                                 |  55%  222 MB
|=========================================                                 |  55%  223 MB
|=========================================                                 |  55%  223 MB
|==========================================                                |  56%  223 MB
|==========================================                                |  56%  224 MB
|==========================================                                |  56%  224 MB
|==========================================                                |  56%  224 MB
|==========================================                                |  56%  225 MB
|==========================================                                |  56%  225 MB
|==========================================                                |  56%  226 MB
|==========================================                                |  56%  226 MB
|==========================================                                |  56%  226 MB
|==========================================                                |  56%  227 MB
|==========================================                                |  57%  227 MB
|==========================================                                |  57%  228 MB
|==========================================                                |  57%  228 MB
|===========================================                               |  57%  228 MB
|===========================================                               |  57%  229 MB
|===========================================                               |  57%  229 MB
|===========================================                               |  57%  230 MB
|===========================================                               |  57%  230 MB
|===========================================                               |  57%  230 MB
|===========================================                               |  57%  231 MB
|===========================================                               |  58%  231 MB
|===========================================                               |  58%  232 MB
|===========================================                               |  58%  232 MB
|===========================================                               |  58%  232 MB
|===========================================                               |  58%  233 MB
|===========================================                               |  58%  233 MB
|===========================================                               |  58%  233 MB
|============================================                              |  58%  234 MB
|============================================                              |  58%  234 MB
|============================================                              |  58%  235 MB
|============================================                              |  59%  235 MB
|============================================                              |  59%  235 MB
|============================================                              |  59%  236 MB
|============================================                              |  59%  236 MB
|============================================                              |  59%  237 MB
|============================================                              |  59%  237 MB
|============================================                              |  59%  237 MB
|============================================                              |  59%  238 MB
|============================================                              |  59%  238 MB
|============================================                              |  59%  238 MB
|============================================                              |  59%  239 MB
|=============================================                             |  60%  239 MB
|=============================================                             |  60%  240 MB
|=============================================                             |  60%  240 MB
|=============================================                             |  60%  240 MB
|=============================================                             |  60%  241 MB
|=============================================                             |  60%  241 MB
|=============================================                             |  60%  242 MB
|=============================================                             |  60%  242 MB
|=============================================                             |  60%  242 MB
|=============================================                             |  60%  243 MB
|=============================================                             |  61%  243 MB
|=============================================                             |  61%  244 MB
|=============================================                             |  61%  244 MB
|==============================================                            |  61%  244 MB
|==============================================                            |  61%  245 MB
|==============================================                            |  61%  245 MB
|==============================================                            |  61%  246 MB
|==============================================                            |  61%  246 MB
|==============================================                            |  61%  246 MB
|==============================================                            |  61%  247 MB
|==============================================                            |  62%  247 MB
|==============================================                            |  62%  248 MB
|==============================================                            |  62%  248 MB
|==============================================                            |  62%  248 MB
|==============================================                            |  62%  249 MB
|==============================================                            |  62%  249 MB
|==============================================                            |  62%  249 MB
|===============================================                           |  62%  250 MB
|===============================================                           |  62%  250 MB
|===============================================                           |  62%  251 MB
|===============================================                           |  63%  251 MB
|===============================================                           |  63%  251 MB
|===============================================                           |  63%  252 MB
|===============================================                           |  63%  252 MB
|===============================================                           |  63%  253 MB
|===============================================                           |  63%  253 MB
|===============================================                           |  63%  253 MB
|===============================================                           |  63%  254 MB
|===============================================                           |  63%  254 MB
|===============================================                           |  63%  255 MB
|================================================                          |  64%  255 MB
|================================================                          |  64%  255 MB
|================================================                          |  64%  256 MB
|================================================                          |  64%  256 MB
|================================================                          |  64%  256 MB
|================================================                          |  64%  257 MB
|================================================                          |  64%  257 MB
|================================================                          |  64%  258 MB
|================================================                          |  64%  258 MB
|================================================                          |  64%  258 MB
|================================================                          |  64%  259 MB
|================================================                          |  65%  259 MB
|================================================                          |  65%  260 MB
|================================================                          |  65%  260 MB
|=================================================                         |  65%  260 MB
|=================================================                         |  65%  261 MB
|=================================================                         |  65%  261 MB
|=================================================                         |  65%  262 MB
|=================================================                         |  65%  262 MB
|=================================================                         |  65%  262 MB
|=================================================                         |  65%  263 MB
|=================================================                         |  66%  263 MB
|=================================================                         |  66%  264 MB
|=================================================                         |  66%  264 MB
|=================================================                         |  66%  264 MB
|=================================================                         |  66%  265 MB
|=================================================                         |  66%  265 MB
|==================================================                        |  66%  265 MB
|==================================================                        |  66%  266 MB
|==================================================                        |  66%  266 MB
|==================================================                        |  66%  267 MB
|==================================================                        |  67%  267 MB
|==================================================                        |  67%  267 MB
|==================================================                        |  67%  268 MB
|==================================================                        |  67%  268 MB
|==================================================                        |  67%  269 MB
|==================================================                        |  67%  269 MB
|==================================================                        |  67%  269 MB
|==================================================                        |  67%  270 MB
|==================================================                        |  67%  270 MB
|==================================================                        |  67%  271 MB
|===================================================                       |  68%  271 MB
|===================================================                       |  68%  271 MB
|===================================================                       |  68%  272 MB
|===================================================                       |  68%  272 MB
|===================================================                       |  68%  273 MB
|===================================================                       |  68%  273 MB
|===================================================                       |  68%  273 MB
|===================================================                       |  68%  274 MB
|===================================================                       |  68%  274 MB
|===================================================                       |  68%  274 MB
|===================================================                       |  69%  275 MB
|===================================================                       |  69%  275 MB
|===================================================                       |  69%  276 MB
|===================================================                       |  69%  276 MB
|====================================================                      |  69%  277 MB
|====================================================                      |  69%  277 MB
|====================================================                      |  69%  277 MB
|====================================================                      |  69%  278 MB
|====================================================                      |  69%  278 MB
|====================================================                      |  69%  279 MB
|====================================================                      |  70%  279 MB
|====================================================                      |  70%  279 MB
|====================================================                      |  70%  280 MB
|====================================================                      |  70%  280 MB
|====================================================                      |  70%  280 MB
|====================================================                      |  70%  281 MB
|====================================================                      |  70%  281 MB
|=====================================================                     |  70%  282 MB
|=====================================================                     |  70%  282 MB
|=====================================================                     |  70%  282 MB
|=====================================================                     |  71%  283 MB
|=====================================================                     |  71%  283 MB
|=====================================================                     |  71%  284 MB
|=====================================================                     |  71%  284 MB
|=====================================================                     |  71%  284 MB
|=====================================================                     |  71%  285 MB
|=====================================================                     |  71%  285 MB
|=====================================================                     |  71%  285 MB
|=====================================================                     |  71%  286 MB
|=====================================================                     |  71%  286 MB
|=====================================================                     |  71%  287 MB
|======================================================                    |  72%  287 MB
|======================================================                    |  72%  287 MB
|======================================================                    |  72%  288 MB
|======================================================                    |  72%  288 MB
|======================================================                    |  72%  289 MB
|======================================================                    |  72%  289 MB
|======================================================                    |  72%  289 MB
|======================================================                    |  72%  290 MB
|======================================================                    |  72%  290 MB
|======================================================                    |  72%  290 MB
|======================================================                    |  73%  291 MB
|======================================================                    |  73%  291 MB
|======================================================                    |  73%  292 MB
|======================================================                    |  73%  292 MB
|=======================================================                   |  73%  292 MB
|=======================================================                   |  73%  293 MB
|=======================================================                   |  73%  293 MB
|=======================================================                   |  73%  294 MB
|=======================================================                   |  73%  294 MB
|=======================================================                   |  73%  294 MB
|=======================================================                   |  74%  295 MB
|=======================================================                   |  74%  295 MB
|=======================================================                   |  74%  296 MB
|=======================================================                   |  74%  296 MB
|=======================================================                   |  74%  296 MB
|=======================================================                   |  74%  297 MB
|=======================================================                   |  74%  297 MB
|========================================================                  |  74%  298 MB
|========================================================                  |  74%  298 MB
|========================================================                  |  74%  298 MB
|========================================================                  |  74%  299 MB
|========================================================                  |  75%  299 MB
|========================================================                  |  75%  299 MB
|========================================================                  |  75%  300 MB
|========================================================                  |  75%  300 MB
|========================================================                  |  75%  301 MB
|========================================================                  |  75%  301 MB
|========================================================                  |  75%  301 MB
|========================================================                  |  75%  302 MB
|========================================================                  |  75%  302 MB
|========================================================                  |  75%  303 MB
|=========================================================                 |  76%  303 MB
|=========================================================                 |  76%  303 MB
|=========================================================                 |  76%  304 MB
|=========================================================                 |  76%  304 MB
|=========================================================                 |  76%  304 MB
|=========================================================                 |  76%  305 MB
|=========================================================                 |  76%  305 MB
|=========================================================                 |  76%  306 MB
|=========================================================                 |  76%  306 MB
|=========================================================                 |  76%  306 MB
|=========================================================                 |  77%  307 MB
|=========================================================                 |  77%  307 MB
|=========================================================                 |  77%  308 MB
|=========================================================                 |  77%  308 MB
|==========================================================                |  77%  308 MB
|==========================================================                |  77%  309 MB
|==========================================================                |  77%  309 MB
|==========================================================                |  77%  310 MB
|==========================================================                |  77%  310 MB
|==========================================================                |  77%  310 MB
|==========================================================                |  78%  311 MB
|==========================================================                |  78%  311 MB
|==========================================================                |  78%  312 MB
|==========================================================                |  78%  312 MB
|==========================================================                |  78%  312 MB
|==========================================================                |  78%  313 MB
|==========================================================                |  78%  313 MB
|===========================================================               |  78%  313 MB
|===========================================================               |  78%  314 MB
|===========================================================               |  78%  314 MB
|===========================================================               |  78%  315 MB
|===========================================================               |  79%  315 MB
|===========================================================               |  79%  315 MB
|===========================================================               |  79%  316 MB
|===========================================================               |  79%  316 MB
|===========================================================               |  79%  317 MB
|===========================================================               |  79%  317 MB
|===========================================================               |  79%  317 MB
|===========================================================               |  79%  318 MB
|===========================================================               |  79%  318 MB
|===========================================================               |  79%  319 MB
|============================================================              |  80%  319 MB
|============================================================              |  80%  319 MB
|============================================================              |  80%  320 MB
|============================================================              |  80%  320 MB
|============================================================              |  80%  320 MB
|============================================================              |  80%  321 MB
|============================================================              |  80%  321 MB
|============================================================              |  80%  322 MB
|============================================================              |  80%  322 MB
|============================================================              |  80%  322 MB
|============================================================              |  81%  323 MB
|============================================================              |  81%  323 MB
|============================================================              |  81%  324 MB
|============================================================              |  81%  324 MB
|=============================================================             |  81%  324 MB
|=============================================================             |  81%  325 MB
|=============================================================             |  81%  325 MB
|=============================================================             |  81%  326 MB
|=============================================================             |  81%  326 MB
|=============================================================             |  81%  326 MB
|=============================================================             |  82%  327 MB
|=============================================================             |  82%  327 MB
|=============================================================             |  82%  328 MB
|=============================================================             |  82%  328 MB
|=============================================================             |  82%  328 MB
|=============================================================             |  82%  329 MB
|=============================================================             |  82%  329 MB
|==============================================================            |  82%  330 MB
|==============================================================            |  82%  330 MB
|==============================================================            |  82%  330 MB
|==============================================================            |  83%  331 MB
|==============================================================            |  83%  331 MB
|==============================================================            |  83%  332 MB
|==============================================================            |  83%  332 MB
|==============================================================            |  83%  332 MB
|==============================================================            |  83%  333 MB
|==============================================================            |  83%  333 MB
|==============================================================            |  83%  333 MB
|==============================================================            |  83%  334 MB
|==============================================================            |  83%  334 MB
|==============================================================            |  83%  335 MB
|===============================================================           |  84%  335 MB
|===============================================================           |  84%  335 MB
|===============================================================           |  84%  336 MB
|===============================================================           |  84%  336 MB
|===============================================================           |  84%  337 MB
|===============================================================           |  84%  337 MB
|===============================================================           |  84%  337 MB
|===============================================================           |  84%  338 MB
|===============================================================           |  84%  338 MB
|===============================================================           |  84%  339 MB
|===============================================================           |  85%  339 MB
|===============================================================           |  85%  339 MB
|===============================================================           |  85%  340 MB
|================================================================          |  85%  340 MB
|================================================================          |  85%  341 MB
|================================================================          |  85%  341 MB
|================================================================          |  85%  341 MB
|================================================================          |  85%  342 MB
|================================================================          |  85%  342 MB
|================================================================          |  85%  343 MB
|================================================================          |  86%  343 MB
|================================================================          |  86%  343 MB
|================================================================          |  86%  344 MB
|================================================================          |  86%  344 MB
|================================================================          |  86%  345 MB
|================================================================          |  86%  345 MB
|=================================================================         |  86%  345 MB
|=================================================================         |  86%  346 MB
|=================================================================         |  86%  346 MB
|=================================================================         |  86%  346 MB
|=================================================================         |  87%  347 MB
|=================================================================         |  87%  347 MB
|=================================================================         |  87%  348 MB
|=================================================================         |  87%  348 MB
|=================================================================         |  87%  348 MB
|=================================================================         |  87%  349 MB
|=================================================================         |  87%  349 MB
|=================================================================         |  87%  349 MB
|=================================================================         |  87%  350 MB
|=================================================================         |  87%  350 MB
|==================================================================        |  88%  351 MB
|==================================================================        |  88%  351 MB
|==================================================================        |  88%  351 MB
|==================================================================        |  88%  352 MB
|==================================================================        |  88%  352 MB
|==================================================================        |  88%  352 MB
|==================================================================        |  88%  353 MB
|==================================================================        |  88%  353 MB
|==================================================================        |  88%  354 MB
|==================================================================        |  88%  354 MB
|==================================================================        |  88%  354 MB
|==================================================================        |  89%  355 MB
|==================================================================        |  89%  355 MB
|==================================================================        |  89%  355 MB
|==================================================================        |  89%  356 MB
|===================================================================       |  89%  356 MB
|===================================================================       |  89%  357 MB
|===================================================================       |  89%  357 MB
|===================================================================       |  89%  357 MB
|===================================================================       |  89%  358 MB
|===================================================================       |  89%  358 MB
|===================================================================       |  89%  358 MB
|===================================================================       |  90%  359 MB
|===================================================================       |  90%  359 MB
|===================================================================       |  90%  359 MB
|===================================================================       |  90%  360 MB
|===================================================================       |  90%  360 MB
|===================================================================       |  90%  360 MB
|===================================================================       |  90%  361 MB
|====================================================================      |  90%  361 MB
|====================================================================      |  90%  362 MB
|====================================================================      |  90%  362 MB
|====================================================================      |  90%  362 MB
|====================================================================      |  91%  363 MB
|====================================================================      |  91%  363 MB
|====================================================================      |  91%  364 MB
|====================================================================      |  91%  364 MB
|====================================================================      |  91%  364 MB
|====================================================================      |  91%  365 MB
|====================================================================      |  91%  365 MB
|====================================================================      |  91%  366 MB
|====================================================================      |  91%  366 MB
|====================================================================      |  91%  366 MB
|=====================================================================     |  92%  367 MB
|=====================================================================     |  92%  367 MB
|=====================================================================     |  92%  367 MB
|=====================================================================     |  92%  368 MB
|=====================================================================     |  92%  368 MB
|=====================================================================     |  92%  369 MB
|=====================================================================     |  92%  369 MB
|=====================================================================     |  92%  369 MB
|=====================================================================     |  92%  370 MB
|=====================================================================     |  92%  370 MB
|=====================================================================     |  92%  370 MB
|=====================================================================     |  93%  371 MB
|=====================================================================     |  93%  371 MB
|=====================================================================     |  93%  372 MB
|======================================================================    |  93%  372 MB
|======================================================================    |  93%  372 MB
|======================================================================    |  93%  373 MB
|======================================================================    |  93%  373 MB
|======================================================================    |  93%  373 MB
|======================================================================    |  93%  374 MB
|======================================================================    |  93%  374 MB
|======================================================================    |  93%  374 MB
|======================================================================    |  94%  375 MB
|======================================================================    |  94%  375 MB
|======================================================================    |  94%  375 MB
|======================================================================    |  94%  376 MB
|======================================================================    |  94%  376 MB
|======================================================================    |  94%  377 MB
|======================================================================    |  94%  377 MB
|=======================================================================   |  94%  377 MB
|=======================================================================   |  94%  378 MB
|=======================================================================   |  94%  378 MB
|=======================================================================   |  94%  378 MB
|=======================================================================   |  95%  379 MB
|=======================================================================   |  95%  379 MB
|=======================================================================   |  95%  379 MB
|=======================================================================   |  95%  380 MB
|=======================================================================   |  95%  380 MB
|=======================================================================   |  95%  380 MB
|=======================================================================   |  95%  381 MB
|=======================================================================   |  95%  381 MB
|=======================================================================   |  95%  382 MB
|=======================================================================   |  95%  382 MB
|=======================================================================   |  95%  382 MB
|=======================================================================   |  95%  383 MB
|========================================================================  |  96%  383 MB
|========================================================================  |  96%  383 MB
|========================================================================  |  96%  384 MB
|========================================================================  |  96%  384 MB
|========================================================================  |  96%  384 MB
|========================================================================  |  96%  385 MB
|========================================================================  |  96%  385 MB
|========================================================================  |  96%  385 MB
|========================================================================  |  96%  386 MB
|========================================================================  |  96%  386 MB
|========================================================================  |  96%  386 MB
|========================================================================  |  97%  387 MB
|========================================================================  |  97%  387 MB
|========================================================================  |  97%  387 MB
|========================================================================  |  97%  388 MB
|========================================================================= |  97%  388 MB
|========================================================================= |  97%  388 MB
|========================================================================= |  97%  389 MB
|========================================================================= |  97%  389 MB
|========================================================================= |  97%  389 MB
|========================================================================= |  97%  390 MB
|========================================================================= |  97%  390 MB
|========================================================================= |  97%  390 MB
|========================================================================= |  98%  391 MB
|========================================================================= |  98%  391 MB
|========================================================================= |  98%  391 MB
|========================================================================= |  98%  392 MB
|========================================================================= |  98%  392 MB
|========================================================================= |  98%  392 MB
|========================================================================= |  98%  393 MB
|========================================================================= |  98%  393 MB
|==========================================================================|  98%  393 MB
|==========================================================================|  98%  394 MB
|==========================================================================|  98%  394 MB
|==========================================================================|  98%  394 MB
|==========================================================================|  99%  395 MB
|==========================================================================|  99%  395 MB
|==========================================================================|  99%  395 MB
|==========================================================================|  99%  396 MB
|==========================================================================|  99%  396 MB
|==========================================================================|  99%  396 MB
|==========================================================================|  99%  397 MB
|==========================================================================|  99%  397 MB
|==========================================================================|  99%  397 MB
|==========================================================================|  99%  398 MB
|==========================================================================|  99%  398 MB
|==========================================================================|  99%  398 MB
|===========================================================================| 100%  398 MB
snps

filter to keep snps where there is data from all samples

snps <- snps %>% 
  filter({select(., matches("[0-9]")) %>% complete.cases() })
snps
snps <- snps %>% 
  mutate(TOTAL_DEPTH= {str_extract(INFO, "DP=[0-9]*") %>% 
      str_remove("DP=") %>%
      as.numeric() }
  ) %>%
  filter(QUAL >=100,
         nchar(ALT)==1,
         TOTAL_DEPTH > quantile(TOTAL_DEPTH, 0.05),
         TOTAL_DEPTH < quantile(TOTAL_DEPTH, 0.95))
snps

unpack the information differnet samples:

samples <- colnames(snps) %>% str_subset("^[0-9]")
for (s in samples) {
snps <- snps %>%
  separate(!!s, into=paste(s,c("gt","tot.depth","allele.depth","ref.depth","ref.qual","alt.depth","alt.qual","gt.lik"),sep="_"),
           sep=":", convert = TRUE)
}
snps

For the MDS we only need the genotype info

gts <- snps %>%
  select(ends_with("_gt"))
gts

convert this to numeric

geno.numeric <- gts %>%
  lapply(factor) %>% # convert charcters to "factors", where each category is internally represented as a number
  as.data.frame() %>% # reformat
  data.matrix() %>%#  convert to numeric
  t() 
head(geno.numeric[,1:5],10)
            [,1] [,2] [,3] [,4] [,5]
X38LTR_gt      2    2    2    2    2
X42LTR_gt      2    3    2    2    2
X42LTRR_gt     2    2    2    2    1
X43LTR_gt      2    2    2    2    2
X43LTRR_gt     2    2    2    2    2
X49LTWR_gt     2    2    2    2    2
X49LTWRR_gt    3    3    3    3    1
X95LTWR_gt     2    3    3    2    2
X95LTWRR_gt    2    3    3    2    2
X99LTWR_gt     2    2    2    2    2
dim(geno.numeric)
[1]     10 134421
dim(gts)
[1] 134421     10
genDist <- as.matrix(dist(geno.numeric))
dim(genDist)
[1] 10 10
#perform the multi-dimensional scaling
geno.mds <- as.tibble(cmdscale(genDist))
geno.mds$ID <- rownames(geno.numeric) 
geno.mds <- geno.mds %>%
  mutate(ID={str_replace(ID, "W", "N") %>%
       str_replace("RR", "R2") %>%
      str_remove_all("(X|_gt)") },
    response=ifelse(str_detect(ID,"N"), "no recovery", "recovery"))
geno.mds
geno.mds %>%
  ggplot(aes(x=V1, y = V2, label=ID, color=response)) +
  geom_point() +
  geom_text_repel(show.legend=FALSE, direction="y")

with LTR_38 removed

convert this to numeric

geno.numeric <- gts %>%
  select(-`38LTR_gt`) %>%
  lapply(factor) %>% # convert charcters to "factors", where each category is internally represented as a number
  as.data.frame() %>% # reformat
  data.matrix() %>%#  convert to numeric
  t() 
head(geno.numeric[,1:5],10)
            [,1] [,2] [,3] [,4] [,5]
X42LTR_gt      2    3    2    2    2
X42LTRR_gt     2    2    2    2    1
X43LTR_gt      2    2    2    2    2
X43LTRR_gt     2    2    2    2    2
X49LTWR_gt     2    2    2    2    2
X49LTWRR_gt    3    3    3    3    1
X95LTWR_gt     2    3    3    2    2
X95LTWRR_gt    2    3    3    2    2
X99LTWR_gt     2    2    2    2    2
dim(geno.numeric)
[1]      9 134421
dim(gts)
[1] 134421     10
genDist <- as.matrix(dist(geno.numeric))
dim(genDist)
[1] 9 9
#perform the multi-dimensional scaling
geno.mds <- as.tibble(cmdscale(genDist))
geno.mds$ID <- rownames(geno.numeric) 
geno.mds <- geno.mds %>%
  mutate(ID={str_replace(ID, "W", "N") %>%
       str_replace("RR", "R2") %>%
      str_remove_all("(X|_gt)") },
    response=ifelse(str_detect(ID,"N"), "no recovery", "recovery"))
geno.mds
geno.mds %>%
  ggplot(aes(x=V1, y = V2, label=ID, color=response)) +
  geom_point() +
  geom_text_repel(show.legend=FALSE, direction="y")
ggsave("../output/MDS.pdf")
Saving 7.29 x 4.51 in image

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